Doofenschmirtz Take Over
by Myron Greenleaf
Summary: Please read the summary located on chapter 1 it is much better than it sounds in my opinion. Finished!
1. Chapter 1: Leaving Prologue

Doofenschmirtz Take Over

Chapter 1: Leaving (Prologue)

**Story Summary: Doofenschmirtz has rebelled against the Freeworld Organization. His Rebellion soon turned into what was later called The Empire with him as its Emperor. The Freeworld Organization was set up to replace the failing United Nations. The Freeworld Organization was defeated in battle after battle against Doofenschmirtz's Imperial Army but retained the vital city of Danville as their stronghold. As the war neared its end, Doofenschmirtz amassed his armies at the gates of the final stronghold of the Freeworld Organization: Danville. Imperial Spies had opened the gates and let the Imperial Armies storming the city in force. Phineas and Ferb are chosen by the citizens and defenders of Danville to escape and later liberate them from The Empire.**

Phineas and Ferb were running. The two of them only had one place in mind. But Right now they were just running away. Doofenschmirtz had won and they had to get away. Leaving everybody to get captured: Linda, Lawrence, Candace, Buford, Baljeet… Isabella. Especially Isabella. Phineas had begged her to leave with them, but she had refused to leave when her Fireside Girls were staying to hold Danville as long as possible. They all knew how much everything depended on Phineas and Ferb leaving Danville. The last Stronghold of the Free World had finally been infiltrated by Imperial Spies and had worked together to finally open the gates for the Imperial Army. Of course there was one place left for them. Great Britain was the last free country on Earth. They had neither joined Doofenschmirtz's Rebellion nor joined the countries of the world in their fight to put down Doofenschmirtz's Rebellion. Great Britain had believed that Doofenschmirtz would win the war and they remained neutral to provide those who lost the war a home away from Doofenschmirtz. But back to Danville and her problem. Everyone from Danville knew that someone had to leave. In fact there wasn't a person in Danville who hadn't voted for Phineas and Ferb to have the honor of Leaving Danville before it was too late.

"Good Bye Danville," Phineas said as he watched his hometown burn during the fighting.

_Phineas's Point of View_

It had been three years since Ferb and I had escaped from the Fall of Danville. When we had arrived in Great Britain, we were immediately praised as heroes for facing the Imperials at almost every turn. **(That's another story.)** Anyway, Great Britain had employed us at different jobs for the future. I was separated from Ferb to hide us from Doofenschmirtz and we went our separate ways for three years. For three years, Ferb and I received training in the field where Great Britain would employ us. After three years, Ferb and I met once more for our first and most likely our only assignment. We were given transport to the Empire where we received a car from the Imperial Government. Ferb was to drive while sat in the Passenger Seat. Of course, there was only one place where we could go. Danville had become the Capital of the Empire. I was to represent Great Britain as an ambassador while Great Britain began planning her own rebellion against the Empire. They studied every single aspect of the Empire that was possible. Ferb meanwhile was trained as a Special Forces Soldier by the British Royal Armed Forces. Sure we were young to represent Great Britain and her interests, but we were the most qualified.


	2. Chapter 2: Return

Chapter 2: Return

"Hey Ferb?" I asked. "How long should it take us to get there?" Ferb shrugged. We had been driving along in the car for a pretty long time heading to Danville.

"What do you think Ferb?" I asked

"About what?" Ferb asked.

"What do you think happened to everybody once we had left?" I clarified.

"Oh. I'm sure they all got out alright, _especially _Isabella," Ferb said teasing me on the last part. I had wanted Isabella to be my girlfriend after we were rescued by Ferb, Baljeet, Candace, Buford, and Irving from Nazi Germany. And yet, after three years, I still defended Isabella at every turn hoping to eventually get the courage to ask her out..

"HEY!" I yelled.

Ferb was laughing very hard, he had trouble concentrating so he pulled over. "I'm *laugh* so *laugh* very *laugh* sorry *laugh*," Ferb said trying desperately to gain control over his voice and the laughing.

"Seriously now," I said. "Do you know why I'm the one being assigned to this job as Ambassador to both the Empire AND the Rebellion?"

"Well, I heard that mom had gotten a job as head of Foreign Relations in The Empire, and Great Britain has figured out who the leader of the Rebellion is, who we both know, which is why you were also given the job as Ambassador to the Rebel Alliance, which the call themselves."

"Hey what happened?" I asked pointing to a truck that had suddenly swerved off the road. "Let's go see if we can't offer some help." We got out and looked around, but we couldn't find anyone so we had turned to head back to the car, when I blinked and found we found ourselves pinned to the ground with a couple guns pointed at us.

"Can a couple of guys try to offer help without the whole pinning us to the ground?" Ferb asked nobody in particular. That was probably for the best because he didn't get an answer.

"Got 'em chief," said a young girl. "So who are you guys?"

"Hey," another girl warned. "They're not armed. Remember the rules."

"I remember them," the first girl said.

"Sorry we saw you guys and panicked. Let me introduce myself," the second girl said. Ferb looked over at me and just rolled his eyes when I was thinking that she looked beautiful…

"My name is Isabella Garcia-Shapiro. General of the Rebellion of the Underground Freeworld," she said. "Now who are you guys?"

"Wait! You said your name was Isabella?" I asked suddenly suspicious.

"Yes… You never answered my question," Isabella responded.

"You mean you don't recognize us?" I asked raising an eyebrow.

"Phineas?" Isabella asked cautiously. I nodded. "IT IS YOU PHINEAS!" she said the last part smiling and she ran up to me and hugged me. "What are you guys doing here?"

"We have jobs," Ferb answered much to my annoyment.

"What jobs are those?" Isabella asked. "You were chosen to escape for a reason! Unless…"

"We have not come back to liberate Danville if that is what you are asking," I said.

"*sigh* Well, it was a hope," Isabella said. "So what are you guys doing here?"

"Well, to put it simply as I am presented to Emperor Doofenschmirtz, I am Phineas Flynn, Ambassador to both The Empire and The Rebellion on behalf of The Kingdom of Great Britain, and this my step-brother and bodyguard Ferb Fletcher," I said. "Does that clear everything up?"

"*sigh* perfectly!" Isabella said.

"Who else?" I asked. Isabella thought about the question for a minute before answering.

"The Fireside Girls left shortly after you did, Django, Baljeet, Buford, Irving, your step-father, and Candace have all made it out alive from Danville if that's what you're wondering." I nodded.

"It is," I said. "Izzy, I really don't want to leave you right now, but if I don't start headed towards Danville again soon, I'm going to be late in my meeting with The Emperor."

"Well we're going back to headquarters," Isabella said. "Django, go with Phineas and do exactly what he tells you, once you are all done with everything, Django will lead you back to Rebellion Headquarters." I nodded, hugging her again while Ferb went to start up the car again.

After another hour in the car and with us catching up on what happened with The Rebellion and whatever else that had happened since Ferb and I had left three years ago, before we had gotten to Danville. We got out and were greeted by none other than the Emperor himself. He quickly noted that I had brought a second person with me and then shrugged off the idea and began introductions.


	3. Chapter 3: Welcome Home

Chapter 3: Welcome Home

_**Phineas's Point of View**_

"Ah, you must be the new Ambassador," Emperor Doofenshmirtz said. "Welcome to Danville."

"Thank You Emperor," I said with courtesy. "It is good to be here after such a long trip."

"As I'm sure it has been," Emperor Doofenshmirtz said. "Come; let me show you the embassy in which you will be staying at."

We walked down the road and I just couldn't help myself but look around. Everything seemed to have only gotten better in the years following the war. While I was gazing at everything in sight, there was an explosion off on the other side of town. "What was that?" Ferb asked.

"Oh it is probably the Alliance. They won't accept defeat at all," Emperor Doofenshmirtz said. Django snickered to himself.

"Hmm, maybe I should go meet the leader of these… what do you call them? Rebel Alliance?" **[1]** I asked. Emperor Doofenshmirtz nodded. "Well, then I think I should really meet them and tell them not to blow up my embassy, I'd rather not be forced to live somewhere where I'm not supposed to be…"

"All is well, your embassy is heavily guarded, none can plant a bomb there," Emperor Doofenshmirtz said.

"Not to be rude Emperor, but your capital of your Empire is being bombed and you have your troops protecting my embassy?" I asked.

"I need you alive for diplomatic negotiations to proceed with Britain," Emperor Doofenshmirtz said.

"Emperor Doofenshmirtz that is exactly the attitude that gets more and more people flocking to the Rebel Banners every day," I said.

"Most likely, but they cannot topple me from power Ambassador," Emperor Doofenshmirtz said.

"Perhaps not, but I hear that there are more than just one group of Rebel's," I said. "Which makes it all the more difficult to put these Rebellions down!"

"Ambassador, I do not believe that you came all the way here from Britain just to talk with me about the Rebellion and its different factions," Emperor Doofenshmirtz said. "Either way, here is your embassy, now I have more important matters to attend to, so until we meet again Ambassador."

I nodded. _He certainly seems to have mellowed since he was leading his armies across most of the world fighting the Freeworld Organization. _I got settled in and Django drove the three of us out of the city limits, claiming that we wanted to explore the countryside before it got too dark and all that nonsense that will get any guard to not question you. He-he, what did my instructor call people like that? I think he called them 'suckers'… Oh well. We drove on to Alliance Headquarters where we were greeted by: Isabella, Buford, Baljeet, Lawrence, Candace, and a few of the fireside girls.

"Hey guys, it's so good to see you all again!" I said getting out of the car.

"Phineas!" Candace shouted and ran up to hug me. Now I understand why Ferb waited a moment to get out of the car…

"Candace, I know that this may sound weird and all, but I can't breathe…" I said gasping for air at the same time.

"Oops," she said moving back towards the others. Greetings like that happened for what felt like ages before Ferb pointed at a clock to show that we were supposed to be leaving.

"Sorry guys, we'll come back as often as we can," I said. Ferb nodded in agreement. We got in the car and began the long trip back to Danville.

"So Ferb, did you notice anything different when you were hanging out with them?"

Ferb shook his head.

"Yeah, I didn't really either," I said content. "So they really haven't changed much."

"Yeah, like your girlfriend!" Ferb said suddenly. I slapped him across the head.

"Will you ever stop doing that?" I asked.

"No," Ferb said starting to laugh.

"I'm tied between calling you the best and the most annoying brother to ever live!" I exclaimed.

"Best," Ferb said smiling.

"Gah!" I said. "Let's just get back to Danville before I get to annoyed with you." Ferb nodded his agreement. He knew that my patience had thinned a little bit ever since we have seen each other for the first time in three years.


	4. Chapter 4: In the end, do things change?

Chapter 4: Over Time, do things change?

**I'm going to try to sooner or later, add a battle or two in, so you know, it becomes more interesting.**

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><p><strong><em>Isabella's Point of View<em>**

Okay, so to make things perfectly clear, Phineas was neutral so far, and as far as anyone could tell, so was Great Britain, which was just perfect because the Alliance needed the backing of Great Britain in order to fight Doofenshmirtz's Army openly.

So over time, Phineas and Ferb would visit as much as possible, he would always lose the spies that were trailing him before coming over. Ferb one day decided to ambush the spies and kill them before they actually found out where the Alliance headquarters was actually located. That probably saved our skin for the time, but it would only be a matter of time before Doofenshmirtz actually figured out where our HQ was and sent an army to annihilate us.

* * *

><p><strong><em>Phineas's Point of View<em>**

"So Ferb," I said as we were barreling down the freeway at 85 miles per hour, but Ferb was the best driver in the world, and he could safely do 120 without crashing, but we didn't want to draw attention to ourselves, so we just went the normal speed of the freeway. "Do you ever regret anything?"

Ferb shook his head. "I know that I do," I said after a few minutes of silence. "I've thought about what happened for so long, that I've finally figured out what I've been missing in my life."

"And what is that?" Ferb asked not taking his eyes off of the road.

"Never getting Isabella as my girlfriend," I admitted. Ferb almost drove us off of the road in complete shock. But luckily, he was a much better driver than that and he was able to get us back on track before we got noticed by the police.

"So you DO know of the crush she's had on you," Ferb said. It was a statement, not a question.

"What crush?" I asked.

"Oh my god," Ferb muttered. "He's a complete idiot!"

"You know, despite popular belief, I can hear very well, and I do know what you just said," Phineas warned.

"Sorry," Ferb apologized. "But what you need to realize is that Isabella has been trying for the last... I don't know... Since we were eight, she's been trying to make you her boyfriend, and now, you finally decide to come out and tell me that you have feelings for Isabella?"

"Yep," I said proudly.

"Oh, I cannot wait to tell Isabella that!" Ferb said laughing.

"Hey no fair!" I pouted. "I was going to talk to her the moment you got to HQ about it!"

"Oh well... In that case, it is you that needs to talk to her," Ferb said disappointed.

"Yeah," I said. _Well, if that keeps him from telling Isabella, then I'm good._

"Well, we're here," Ferb said pulling into the garage that Rebel Soldiers were guarding.

"You know, that this hideout is so obvious, its a wonder why Doofenshmirtz doesn't know it is here," I said amazed.

"It is kinda sad that he doesn't know, but just as well for us, because this way, we can see our friends whenever we want to without having to travel long distances or take large amounts of time off of working to go and see them," Ferb said getting out of the car.

Isabella was waiting patiently for us when we arrived like she always is, with Linda Flynn-Fletcher, Lawrence Fletcher, Candace Flynn, and a few others. "Hey Phineas."

"Hey Isabella," I said glancing at Ferb who nodded encouragingly. "Can I talk to you privately?"

"Uh... sure...?" Isabella said/asked understandably confused. We walked into a private room where no one would bother us. "So what do you need to talk to me about?"

"Um... I... I..." I stuttered.

"It's okay Phineas," Isabella said soothingly. "You know that you can tell me anything and I'll help you if I can."

"I... I love you Isabella," I finally managed to say. Whatever Isabella was thinking it wasn't that... She was visibly shocked and shaken by the sudden declaration of emotion.

"Well, it took you long enough," Isabella finally managed to say with a smile. I smiled also already knowing that she loved me back.

"Isabella Garcia-Shapiro, will you be my girlfriend?" I asked timidly.

Isabella rolled her eyes. "Of course Phineas!" she said cheerfully. With that, we walked out to where everyone was waiting patiently. They obviously knew something was up, because Isabella looked considerably happier than before.

"Well, I'm sure that whatever you two talked about, it was satisfyingly pleasing for Isabella, because she looks like she just woke up from one of her dreams where she and Phineas were married," Candace commented.

"And how would you know what I look like when I wake up from dreaming about me and Phineas being married?" Isabella challenged.

"I have my sources," Candace replied before turning to Ferb and striking up a conversation with him. I rolled my eyes. _Typical._

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><p>We had another pretty average day after me asking Isabella to be my girlfriend and all that. I'm sure that everyone knew about her being my girlfriend and all, but I don't care, I have the love of my life as my girlfriend, and as soon as this war is over, we can settle down and have a normal family again. And when I mean family, I am of course talking about, my family, her family, our friends, not worrying about war in any way, all we are worried about is what we plan to do for the next day.<p>

"Isabella?" I asked as we were staring at plans for an armed incursion into Danville that just MIGHT put an immediate end to the Doofenshmirtz Empire.

"Mhm?" Isabella responded, not really paying much attention.

"When do you think that the war will truly end?" I asked. "I mean, if Doofenshmirtz is dead and all of that, there are sure going to be his generals who will refuse your demands to surrender without a fight and all of that, so in essence, you will be fighting to retake the entire world, minus Danville and Great Britain, and Ireland."

"I don't know," Isabella admitted. "This war may not end in our lifetimes Phineas, but we can all hope that it will end soon, so we can have a normal relationship."

"Isabella, when have we ever had a normal relationship?" I asked rhetorically. "I mean, our entire friendship started with Ferb and I building some giant contraption in our backyard."

"Good point, but in our terms, it is as normal as it is going to get," Isabella pointed out.

"On that we can both agree on," I conceded.

I looked out at the sky and wondered if we truly would see the end of the war.

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><p><strong>FINALLY! This marks the end of my story on Doof Take Over. I know, only four chapters and all of that, but I'm making a sequel to this story. The next story will have the battles that begin the "Reconquista" of earth. <strong>

**Look at my profile because sooner or later, it will tell you what the sequel name is... I am open to suggestions as reviews for this story, in fact, the four top story names, I will post a poll on my profile for. I thank you all for reading this story... And a happy mother's day to you all!  
><strong>


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